Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment

Nucleic Acids Res. 2015 Mar 31;43(6):3128-42. doi: 10.1093/nar/gkv182. Epub 2015 Mar 9.


The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA-null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adaptive Immunity / genetics
  • B-Lymphocytes / immunology
  • B-Lymphocytes / metabolism
  • Base Sequence
  • Binding Sites / genetics
  • CRISPR-Cas Systems
  • Cell Line
  • Chromatin Immunoprecipitation
  • Conserved Sequence
  • Gene Expression Regulation
  • Genes, MHC Class II
  • Genome, Human
  • Histones / metabolism
  • Humans
  • Nuclear Proteins / deficiency
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • Protein Binding
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Trans-Activators / deficiency
  • Trans-Activators / genetics
  • Trans-Activators / metabolism*


  • Histones
  • MHC class II transactivator protein
  • Nuclear Proteins
  • RNA, Messenger
  • Trans-Activators